Source code for pysisyphus.calculators.Composite

import numpy as np
import sympy as sym

# from sympy import sympify, lambdify,

from pysisyphus.calculators.Calculator import Calculator

from pysisyphus.calculators import ORCA, Turbomole, DFTD4

    "dftd4": DFTD4.DFTD4,
    "orca": ORCA.ORCA,
    "turbomole": Turbomole.Turbomole,
    from pysisyphus.calculators import PySCF

    CALC_CLASSES["pyscf"] = PySCF.PySCF
except (ModuleNotFoundError, OSError):

[docs] class Composite(Calculator): def __init__( self, final, keys_calcs=None, calcs=None, remove_translation=False, **kwargs ): # Either directly supply a dictionary with Calculator objects (key_calcs) # or a dictionary containing information to set up calculators. assert keys_calcs or calcs super().__init__(**kwargs) if calcs: keys_calcs = {} calc_kwargs_ = { "charge": self.charge, "mult": self.mult, "pal": self.pal, "mem": self.mem, } for i, (key, kwargs) in enumerate(calcs.items()): calc_kwargs = calc_kwargs_.copy() calc_kwargs["calc_number"] = i calc_kwargs["base_name"] = f"composite_{key}" # Don't modify original dict kwargs = kwargs.copy() type_ = kwargs.pop("type") calc_kwargs.update(**kwargs) calc_cls = CALC_CLASSES[type_] keys_calcs[key] = calc_cls(**calc_kwargs) self.keys_calcs = keys_calcs assert all([key in final for key in self.keys_calcs.keys()]) = final self.remove_translation = remove_translation # The energies are just numbers that we can easily substitute in self.energy_expr = sym.sympify( # The forces/Hessians are matrices that we can't just easily substitute in. self.arr_args = sym.symbols(" ".join(self.keys_calcs.keys())) self.arr_expr = sym.lambdify(self.arr_args, self.energy_expr)
[docs] def get_final_energy(self, energies): return float(self.energy_expr.subs(energies).evalf())
[docs] def get_energy(self, atoms, coords, **prepare_kwargs): energies = {} for key, calc in self.keys_calcs.items(): energy = calc.get_energy(atoms, coords, **prepare_kwargs)["energy"] energies[key] = energy final_energy = self.get_final_energy(energies) results = { "energy": final_energy, } return results
[docs] def get_forces(self, atoms, coords, **prepare_kwargs): energies = {} forces = {} for key, calc in self.keys_calcs.items(): results = calc.get_forces(atoms, coords, **prepare_kwargs) energies[key] = results["energy"] forces[key] = results["forces"] keys = self.keys_calcs.keys() for key in keys: self.log(f"|forces_{key}|={np.linalg.norm(forces[key]):.6f}") self.log("") final_energy = self.get_final_energy(energies) final_forces = self.arr_expr(**forces) # Remove overall translation if self.remove_translation: f3d = final_forces.reshape(-1, 3) f3d -= f3d.mean(axis=0)[None, :] results = { "energy": final_energy, "forces": final_forces, } return results
[docs] def get_hessian(self, atoms, coords, **prepare_kwargs): energies = {} hessians = {} for key, calc in self.keys_calcs.items(): results = calc.get_hessian(atoms, coords, **prepare_kwargs) energies[key] = results["energy"] hessians[key] = results["hessian"] final_energy = self.get_final_energy(energies) final_hessian = self.arr_expr(**hessians) results = { "energy": final_energy, "hessian": final_hessian, } return results
[docs] def run_calculation(self, atoms, coords, **prepare_kwargs): return self.get_energy(atoms, coords, **prepare_kwargs)